Then came the double-take, for thousands of New Yorkers, camera-toting tourists, maintenance workers and residents gazing out the window as they sipped their morning coffee: The flags above the Brooklyn Bridge are not white.

At least, not usually.

The bridge, a landmark so iconic it is frequently one of the first structures to be smashed to pieces in apocalyptic movies, always flies enormous American flags above its two towers.

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Surveillance footage shows a group crossing the bridge around 3:10 a.m., shortly before the lights illuminating the flags on both towers went out, said John Miller, the Police Department’s deputy commissioner of intelligence. What appeared to be large aluminum pans, like those to cook lasagna for a crowd, had apparently been used to cover the lights.

Those responsible probably had some climbing experience, perhaps even on bridges, Miller said.

“At this time, no particular nexus to terrorism or politics,” he said. “This could be someone’s art project or someone’s statement. We’re just not clear what that statement is.”

They were not alone.

Robert Langdon, the fictional Harvard symbologist of “The Da Vinci Code,” would have had a field day with the stunt. The white flag of surrender seemed the obvious allusion, until it emerged that the flags were actually bleached Old Glories, raising confused questions of patriotism and politics.

Then there was the choice of the Brooklyn Bridge.

“I suspect a protest,” as Mike Hout, 64, a resident of the Dumbo neighborhood, put it, “but of what?”

An officer on the bridge told Carolyn Peterson that the police initially thought a film shoot in Dumbo might be responsible, but the film crew had denied involvement, Peterson said.

“Aliens,” declared someone named Alex, on Twitter.

“Manhattan surrendering to Brooklyn,” suggested Rebecca Mead, a writer for The New Yorker.

Others proposed a connection to politics - a show of strength from Gov. Andrew M. Cuomo, perhaps – or a power grab by Letitia James, the public advocate, who has not so subtly explored the possibility of assuming some of the mayor’s powers while he vacations in Italy. (James said on Tuesday that she was “deeply concerned” about the security breach.)

But no conspiracy theory was given more credence – at least initially – than the announcement, by the Twitter account @BicycleLobby, that it had hoisted white flags “to signal our complete surrender of the Brooklyn Bridge bicycle path to pedestrians.” The post was a joke, news organizations that had taken it at face value discovered to their chagrin.

The authorities were at a loss on Tuesday morning. Asked to explain the situation, a spokesman for the Police Department, Detective Martin Speechley, reported this: “There’s a white flag on the Brooklyn Bridge.”

Were they investigating? “Course, yeah.”

The bridge has suffered more than its share of indignities over the years, including, most recently, the “locks of love” - affixed by couples – that the Transportation Department has deemed a safety hazard. But it has also been a al-Qaida target: The mastermind of the Sept. 11 attacks, Khalid Sheikh Mohammed, once told an operative to destroy the bridge by cutting its suspension cables.

Now cameras and marked police cars guard the entrances. A police boat lurks nearby in the East River. Round-the-clock security cameras watch the point on shore where the suspension cables are anchored.

Eric Adams, the Brooklyn borough president, offered a $5,000 reward on Tuesday for information about the perpetrators out of his own pocket, saying that if it was a prank, “I’m not laughing.”

On the bridge, New Yorkers and tourists veered between fear, puzzlement and absurdist humor.

“The first thing I told myself is, ‘That’s a warning sign,’ ” said Jeffrey Brown, 37, who sells water and Gatorade on the bridge. “Where’s your security at?”

Nearby, Nick Krevatas, one of the workers who were to hoist the new 12-by-18-foot red, white and blue flags that arrived in a Transportation Department truck by early afternoon, pulled on an elaborate harness.

“I feel we’ve been tampered with on our soil,” he said, a fat cigar clamped in the corner of his mouth. (He was still smoking it as he walked up the suspension cable to the towers.)